Constant pH simulations with the coarse-grained MARTINI model-Application to oleic acid aggregates

Canadian Journal of Chemistry

Volumn 91, Issue 9, 2013, Pages 839-846

  Bennett, W F Drew ^a   Chen, Alexander W ^a   Donnini, Serena ^b   Groenhof, Gerrit ^c   Tieleman, D Peter ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^c UNIVERSITY OF JYVÄSKYLÄ   (Finland)

Author keywords

Coarse grained model; Constant pH molecular dynamics; Fatty acids; MARTINI model; Oleic acid

Indexed keywords

AGGREGATION BEHAVIOR; COARSE GRAINED MODELS; CONSTANT PH MOLECULAR DYNAMICS; DIOLEOYLPHOSPHATIDYLCHOLINE; IONIZABLE MOLECULES; LONG CHAIN FATTY ACID; RUNNING SIMULATIONS; SURFACTANT PHASE BEHAVIOR;

AGGREGATES; FATTY ACIDS; INDUSTRIAL APPLICATIONS; LIPID BILAYERS; MICELLES; MOLECULAR DYNAMICS; MOLECULES; OLEIC ACID;

COMPUTER SIMULATION;

EID: 84884197976     PISSN: 00084042     EISSN: None     Source Type: Journal    
DOI: 10.1139/cjc-2013-0010     Document Type: Article

References (37)

1. Markvoort A. J. Pfleger N. Staffhorst R. Hilbers P. A. J. Van Santen R. A. Killian J. A. De Kruijff B. Biophys. J. 2010, 99, 1520. 10.1016/j.bpj.2010. 06.057.
2. Chen I. A. Szostak J. W. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7965. 10.1073/pnas.0308045101.
3. Fedorenko A. Lishko P. V. Kirichok Y. Cell 2012, 151, 400. 10.1016/j.cell.2012.09.010.
4. Severin F. F. Severina I. I. Antonenko Y. N. Rokitskaya T. I. Cherepanov D. A. Mokhova E. N. Vyssokikh M. Y. Pustovidko A. V. Markova O. V. Yaguzhinsky L. S. Korshunova G. A. Sumbatyan N. V. Skulachev M. V. Skulachev V. P. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 663. 10.1073/pnas.0910216107.
5. Ponnurangam S. Chernyshova I. V. Somasundaran P. Langmuir 2012, 28, 10661. 10.1021/la300995g.
6. Fischer C. L. Drake D. R. Dawson D. V. Blanchette D. R. Brogden K. A. Wertz P. W. Antimicrob. Agents Chemother. 2012, 56, 1157. 10.1128/AAC.05151-11.
7. Cistola D. P. Hamilton J. A. Jackson D. Small D. M. Biochemistry 1988, 27, 1881. 10.1021/bi00406a013.
8. Cistola D. P. Atkinson D. Hamilton J. A. Small D. M. Biochemistry 1986, 25, 2804. 10.1021/bi00358a011.
9. Budavari, S. Inc., Whitehouse Station, NJ, 1996.
10. Notman R. Noro M. G. Anwar J. J. Phys. Chem. B 2007, 111, 12748. 10.1021/jp0723564.
11. Turner D. C. Yin F. Kindt J. T. Zhang H. Langmuir 2010, 26, 4687.
12. King D. T. Warren D. B. Pouton C. W. Chalmers D. K. Langmuir 2011, 27, 11381. 10.1021/la2022903.
13. Ngo V. A. Kalia R. K. Nakano A. Vashishta P. J. Phys. Chem. B 2012.
14. Cerezo J. Zuniga J. Bastida A. Requena A. Ceron-Carrasco J. P. J. Phys. Chem. B 2011, 115, 11727. 10.1021/jp203498x.
15. Morrow B. H. Wang Y. Wallace J. A. Koenig P. H. Shen J. K. J. Phys. Chem. B 2011, 115, 14980. 10.1021/jp2062404.
16. Morrow B. H. Koenig P. H. Shen J. K. J. Chem. Phys. 2012, 137, 194902. 10.1063/1.4766313.
17. Mongan J. Case D. A. McCammon J. A. J. Comput. Chem. 2004, 25, 2038. 10.1002/jcc.20139.
18. Lee M. S. Salsbury F. R. Brooks C. L. Proteins: Struct., Funct., Bioinform. 2004, 56, 738. 10.1002/prot.20128.
19. Khandogin J. Brooks C. L. III. Biophys. J. 2005, 89, 141. 10.1529/biophysj.105.061341.
20. Donnini S. Tegeler F. Groenhof G. Grubmüller H. J. Chem. Theory Comput. 2011, 7, 1962. 10.1021/ct200061r.
21. Borjesson U. Hünenberger P. H. J. Chem. Phys. 2001, 114, 9706. 10.1063/1.1370959.
22. Shih A. Y. Arkhipov A. Freddolino P. L. Schulten K. J. Phys. Chem. B 2006, 110, 3674. 10.1021/jp0550816.
23. Kasson P. M. Kelley N. W. Singhal N. Vrljic M. Brunger A. T. Pande V. S. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11916. 10.1073/pnas.0601597103.
24. Marrink S. J. de Vries A. H. Tieleman D. P. Biochim. Biophys. Acta Biomem. 2009, 1788, 149. 10.1016/j.bbamem.2008.10.006.
25. Baoukina S. Marrink S. J. Tieleman D. P. Biophys. J. 2012, 102, 1866. 10.1016/j.bpj.2012.03.048.
26. Shinoda W. Devane R. Klein M. Molecular Simulation 2007, 33, 27. 10.1080/08927020601054050.
27. Marrink S. J. Risselada H. J. Yefimov S. Tieleman D. P. de Vries A. H. J. Phys. Chem. B 2007, 111, 7812. 10.1021/jp071097f.
28. Yesylevskyy S. O. Schäfer L. V. Sengupta D. Marrink S. J. PLoS Comput. Biol. 2010, 6, e1000810. 10.1371/journal.pcbi.1000810.
29. Berendsen H. J. C. Postma J. P. M. Van Gunsteren W. F. Dinola A. Haak J. R. J. Chem. Phys. 1984, 81, 3684. 10.1063/1.448118.
30. Van der Spoel D. Lindahl E. Hess B. Groenhof G. Mark A. E. Berendsen H. J. J. Comput. Chem. 2005, 26, 1701. 10.1002/jcc.20291.
31. Berendsen H. J. C. Van der Spoel D. Van Drunen R. Comput. Phys. Commun. 1995, 91, 43. 10.1016/0010-4655(95)00042-E.
32. Kirkwood J. G. J. Chem. Phys. 1935, 3, 300.
33. MacCallum J. L. Bennett W. Tieleman D. P. Biophys. J. 2008, 94, 3393. 10.1529/biophysj.107.112805.
34. Ptak M. Egret-Charlier M. Sanson A. Bouloussa O. Biochim. Biophys. Acta Biomem. 1980, 600, 387. 10.1016/0005-2736(80)90442-3.
35. Small D. M. Cabral D. J. Cistola D. P. Parks J. S. Hamilton J. A. Hepatology 1984, 4, 77S. 10.1002/hep.1840040814.
36. Bennett W. F. D. Tieleman D. P. J. Chem. Theory Comput. 2011, 7, 2981. 10.1021/ct200291v.
37. de Jong D. H. Singh G. Bennett W. F. D. Arnarez C. Wassenaar T. A. Schäfer L. V. Periole X. Tieleman D. P. Marrink S. J. J. Chem. Theory Comput. 2012, 9, 687. 10.1021/ct300646g.